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SAMtools

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that is

  • flexible enough to store all the alignment information generated by various alignment programs

  • simple enough to be easily generated by alignment programs or converted from existing alignment formats

  • compact in file size

  • allows most of operations on the alignment to work on a stream without loading the whole alignment into memory

  • allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Usage

SAMtools can be activated using the module file:

module load apps/SAMtools/1.7/gcc-4.9.4

Note: The module file also loads the compiler gcc/4.9.4.

Test

  1. Download the following example files using:

    cd some_directory
    cp -r /usr/local/packages/apps/SAMtools/1.7/gcc-4.9.4/examples .
    cd examples
    # sample data
    # ex1.fa - contains 2 sequences cut from the human genome
    # ex1.sam.gz - contains MAQ alignments
    # 00README.txt contains instructions and description of results
    samtools #gives a list of options
    samtools faidx ex1.fa #index the reference FASTA
    samtools view -S -b -t ex1.fa.fai -o ex1.bam ex1.sam.gz #convert SAM to BAM
    samtools index ex1.bam #build index for BAM
    samtools view ex1.bam seq2:450-550 #view a portion of BAM file
    samtools tview -p seq2:450 ex1.bam exl.fa #visually inspect alignments at same location
    samtools mpileup -f ex1.fa ex1.bam #view data in pileup format
    samtools mpileup -vu -f ex1.fa ex1.bam > ex1.vcf #generate uncompressed VCF file of variants
    samtools mpileup -g -f ex1.fa ex1.bam > ex1.bcf #generate compressed VCF file of variants
    

Installation notes

SAMtools was compiled using the install_SAMtools.sh script, the module file is /usr/local/modulefiles/apps/SAMtools/1.7/gcc-4.9.4.